SAXSdb — 1avc

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ANNEXIN VI

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–618	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；VAPOUR DIFFUSION (HANGING DROP), SODIUM ACETATE 1.2 M AS PRECIPITANT, POTASSIUM CACODYLATE 0.1 M, PH 6.5, CALCIUM CHLORIDE 6.2 MM ROOM TEMPERATURE, vapor diffusion - hanging drop	Resolution 2.90 Å R-free 0.268

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	ANXA6_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 56–673； UniProt 1–618

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1avc
Deposition date deposition_date	1997-09-16
Structure title title	BOVINE ANNEXIN VI (CALCIUM-BOUND)
Keywords keywords	ANNEXIN, CALCIUM-BINDING, MEMBRANE-BINDING, CALCIUM/PHOSPHOLIPID-BINDING PROTEIN, CALCIUM-PHOSPHOLIPID-BINDING PROTEIN complex; CALCIUM/PHOSPHOLIPID-BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.21 Å
Radius of gyration Rg (electron density) rg_electron	28.41 Å
Forward intensity I(0) i0	86666100.00
Molecular weight molecular_weight	72997.0 kDa
Excluded volume excluded_volume	91344 Å³
Envelope volume envelope_volume	109970 Å³
Hydration-shell volume shell_volume	33101 Å³
Envelope diameter envelope_diameter	100.5 Å
Shell Rg shell_rg	34.69 Å
Envelope Rg envelope_rg	28.40 Å
Shape Rg shape_rg	28.43 Å
Total Rg total_rg	28.95 Å
Total atoms total_atoms	5114
Residues n_residues	642
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	97.9 Å
Rg (real space) rg_real	29.21 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	8.6670e+07
I(0) uncertainty (real space) i0_real_error	1.2410e+06
Rg (reciprocal space) rg_reciprocal	29.21 Å
I(0) (reciprocal space) i0_reciprocal	86670000.0000
Solution quality estimate total_estimate	0.8861
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.4 Å
Skewness Skewness skewness	0.336
Kurtosis Kurtosis kurtosis	-0.366
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16170000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.926

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ANNEXIN VI
Molecular weight formula_weight	76011.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5231

MAKIAQGAKYRGSIRDFPDFNPSQDAETLYNAMKGFGSDKEAIINLITSRSNKQRQEICQNYKSLYGKDLIADLKYELTGKFERLIVGLMRPPAYADAKEIKDAISGIGTDEKCLIEILASRTNEQIHQLVAAYKDAYERDLEADITGDTSGHFRKMLVVLLQGTREEDDVVSEDLVQQDVQDLYEAGELKWGTDEAQFIYILGNRSKQHLRLVFDEYLKTTGKPIEASIRGELSGDFEKLMLAVVKCIRSTAEYFAERLFKAMKGLGTRDNTLIRIMVSRSELDMLDIREIFRTKYEKSLYSMIKNDTSGEYKKTLLKLCGGDDDAAGQFFPEAAQVAYQMWELSAVARVELKGTVRPAGDFNPDADAKALRKAMKGLGTDEDTIIDIITHRSNAQRQQIRQTFKSHFGRDLMADLKSELSGDLARLILGLMMPPAHYDAKQLKKAMEGAGTDEKALIEILATRTNAEIQAINKAYKEDYHKTLEDALSSDTSGHFKRILISLATGNREEGGEDRERAREDAQVAAEILEIADTTSGDKSSLETRFMMILCTRSYPDLRRVFQEFVKMTNYDVEHTIKKEMSGDVRDVFVAIVQSVKNKPLFFADKLYKSMKGAGTEEKTLTRIMVSRSEIDLLNIRREFIEKYDKSLHQAIEGDTSGHFLKALLAICGGED

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	117

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1avca1
Class class	a — All alpha proteins
Fold Fold fold	a.65 — Annexin
Superfamily Superfamily superfamily	a.65.1 — Annexin
Family Family family	a.65.1.1 — Annexin

Domain ID domain_id	d1avca2
Class class	a — All alpha proteins
Fold Fold fold	a.65 — Annexin
Superfamily Superfamily superfamily	a.65.1 — Annexin
Family Family family	a.65.1.1 — Annexin

CATH v4.4 (8 domains)

Domain ID domain_id	1avcA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1avcA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1avcA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1avcA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1avcA05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1avcA06
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1avcA07
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1avcA08
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

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8. Citations (2)

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Unit-cell length a length_a	67.404 Å
Unit-cell length b length_b	67.404 Å
Unit-cell length c length_c	200.078 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2680

fit	/app/data/saxs_computation/av/1avc/1avc.fit
pddf	/app/data/pr_computation/av/1avc/1avc.pr.out
profile	/app/data/saxs_computation/av/1avc/1avc.dat

BOVINE ANNEXIN VI (CALCIUM-BOUND)

1. Protein Identity and Related Structures Protein Identity & Related Structures

ANNEXIN VI

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction